Imaging the dynamic influence of functional groups on metal-organic frameworks

Metal-organic frameworks (MOFs) with different functional groups have wide applications, while the understanding of functionalization influences remains insufficient. Previous researches focused on the static changes in electronic structure or chemical environment, while it is unclear in the aspect of dynamic influence, especially in the direct imaging of dynamic changes after functionalization. Here we use integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM) to directly ‘see’ the rotation properties of benzene rings in the linkers of UiO-66, and observe the high correlation between local rigidity and the functional groups on the organic linkers. The rigidity is then correlated to the macroscopic properties of CO2 uptake, indicating that functionalization can change the capability through not only static electronic effects, but also dynamic rotation properties. To the best of our knowledge this is the first example of a technique to directly image the rotation properties of linkers in MOFs, which provides an approach to study the local flexibility and paves the way for potential applications in capturing, separation and molecular machine.


Reviewer #1
The manuscript entitled "Imaging the Dynamic Influence of Functional Groups on Metal Organic Frameworks" by Tiefeng Wang et al. presents a novel approach that combines iDPC-STEM experimental and first-principles techniques to investigate the rotation properties of various functional groups in the linkers of UiO-66-X. The study also examines the impact of these functional groups on the local rigidity of the framework with respect to CO2 capture.
One notable finding is the presence of functional benzene rings in the UiO-66 channels with distinct rotation properties, suggesting that the structural flexibility of the framework can be modulated by controlling the orientation of these functional groups. Furthermore, the manuscript highlights the impressive relationship between flexibility and local rigidity with CO2 capture, which has important implications for optimizing the efficiency of CO2 adsorption in metal organic frameworks.
However, there are some questions should be addressed prior to further evaluation 1) To promote consistency and clarity throughout the manuscript, it would be beneficial to include color descriptions for each icon in the atomic models presented in the figures. Specifically, it is recommended to follow the example set in Figure 4, where the color-coded icons are described in the legend.
Authors Reply: We thank the reviewer for the constructive suggestions. We added the descriptions in figure legends.   and . (b, e) iDPC-STEM images of  and   from [110] orientation. The FFT pattern is shown as inset. (c, f) Magnified iDPC-STEM images and simulated results of  and  The scale bar is 1 nm. The grey, red, white, blue and brown atoms represent C,O,H,N and Br elements,respectively." (Page 16) 2) In regard to Figure 2f and Figure 3e, it appears that the intensity of the center benzene ring in the simulated iDPC-STEM image appears slightly weaker than the four surrounding rings. This difference in intensity may be unexpected, it may be worthwhile for the authors to investigate this issue further and ensure that the simulated images accurately reflect the expected intensity of the benzene rings.

Authors Reply:
The weaker intensity is attributed to the signal broadening caused by the rotation of benzene, and the stronger intensity of surrounding linkers is observed because we did not change the rotation orientations of these linkers during the simulation. For the simulation, we build a three- 3) In Figure 3 and Figure S7, it appears that the iDPC-STEM images of  . 3a), and the revised figure is shown below. The results of average FWHM and corresponding discussion remain the same.    and  4) In addition to discussing the full width at half maximum (FWHM) of the intensity profile, it would also be beneficial to examine the peaks of the line profile in more detail.

Authors Reply:
We have analyzed the intensity profile in our previous works and identified the position of carbon atoms in BDC-X linkers (Nano Lett. 2023, 23, 1787−1793. Other works have also used iDPC-STEM to reveal the local distortion of UiO-66 (Nano Lett. 2022, 24, 9928-9934).
In this work, we focused on the rotation properties of benzene ring in BDC-X linkers. Therefore, we mainly studied the FWHM of the intensity profile. In the revised manuscript, we added some discussion on the peak position and the peak shape in the line profiles.
"For UiO-66-Br, however, the signals of BDC-Br are blurred from a narrow line to a larger bright spot (Fig. 2f). The asymmetric peak shape indicates that the functional groups of -Br may be biased in one direction. Moreover, the FWHM along the long axis increased to 4.02 Å. The broadening effect is attributed to the π-flipping of benzene rings in the BDC-Br linkers." (Page 7)

Reviewer #2
This manuscript tries to show the aspect of dynamic influence, especially in the direct imaging of dynamic changes after functionalization of MOFs, in order to see correlation between local rigidity and the functional groups on the organic linkers. The (iDPC-STEM) images are beautiful and wellcombined with the measurement of FWHM in a rigorous manner and supported by a DFT study.
However, this study is focused on pristine materials without the interactions of the MOFs with CO2 provide the best values for CO2 uptake. In this sense, the proposed relationship of rotation energy and CO2 uptake does not fix suitable (see Figure 5c), this is not well supported with these data.
Authors need to carry out an in-situ study of CO2 sorption that reinforces this hypothesis. For instances, inelastic-and quasi-elastic neutron scattering is one of the most accurate techniques to study it (Chem. Sci., 2017, 8, 3109-3120). This paper is not suitable for Nature Communications.
Authors Reply: We thank the reviewers for their recognition of our images and studies, as well as for their valuable suggestions. Our work focused more on the use of iDPC-STEM to image the dynamic properties of UiO-66 with different functional groups. At the end of our work, we found a relationship between local rigidity and CO2 uptake. It can partially explain the different CO2 capture capability of UiO-66-X, but the detailed mechanism requires further investigation. Finally, the recommendations are inspiring and we added the two references in the revised manuscript. We agree that more investigation is required to further reveal the mechanism between rigidity and CO2 capture of UiO-66-X. In situ inelastic-and quasi-elastic neutron scattering is one of the most accurate techniques for a better understanding of the mechanism, which could provide detailed information of the lattice dynamics and molecular vibrations.
To address the issues raised by the reviewer, we made the following revisions to the text and added Fig. S12 in SI.

Reviewer #3
This manuscript used iDPC-STEM to characterize the dynamic properties of MOFs, which is novel and interesting. The authors analyzed the π-flipping properties of UiO-66 with different functional groups and systematically studied the influences on the MOF flexibility. The local rigidity of MOFs are also correlated with the CO2 capacity. This work is appealing and inspiring. Therefore, I suggest that this manuscript can be published in Nature Communications with a minor revision. The following are detailed suggestions.
1. The authors used TEM simulations to correlate with the experimental images. The simulation details were described in the main text, but it is not intuitive. Some supporting figures should be added to better illustrate the simulated models.
Authors Reply: We thank the review for valuable suggestions. We added the detailed description of the simulation in SI, and provided a model figure for the simulated regions.  2. The authors fitted the FWHM against the calculated rotation energy in Fig. 5. Although the values of fitted parameters were reported, the error range is not included. I recommend the authors to add this into SI.
Authors Reply: We added the error range of fitted parameters in SI. 3. The authors mentioned that NMR can be used to characterize the benzene rotation of BDC linkers.
And in this work, the authors proposed that iDPC-STEM can also characterize the flexibility of Authors Reply: After structural optimization, we found that the structure of UiO-66-NH2 and UiO-66-CH3 remained unchanged (Fig. S10). The BDC-X linkers are basically the same, while the intramolecular hydrogen bonds had significantly different length. The different strength of hydrogen bonds affected the rotation properties, which was discussed in the 'theoretical explanations' section in Page 9. For clarification, we added a supplementary figure (Fig. S10) to better illustrate the structure of BDC-CH3 and BDC-NH2.
"This is attributed to the intramolecular hydrogen bond of BDC-NH2 and BDC-OH (Fig. S10)

REVIEWERS' COMMENTS
Reviewer #1 (Remarks to the Author): The authors have addressed all my concerns. I think the paper is now suitable for publication.
Reviewer #2 (Remarks to the Author): This manuscript tries to show the aspect of dynamic influence, especially in the direct imaging of dynamic changes after functionalization of MOFs, in order to see correlation between local rigidity and the functional groups on the organic linkers. The (iDPC-STEM) imagens are beautiful and wellcombined with the measurement of FWHM in a rigorous manner and supported by a DFT study. This study has been improved during the revision step. In my opinion, this manuscript is currently suitable for publication in Nature Communications. The authors have made a great effort to address the issues raised by the all referees. I am happy to recommend the publication of the manuscript in its current form.
Reviewer #3 (Remarks to the Author): The authors have adequately addressed the concerns raised and the quality of the manuscript have been improved after the revision. It could be accepted in its current form.

Reviewer #1
The manuscript entitled "Imaging the Dynamic Influence of Functional Groups on Metal Organic Frameworks" by Tiefeng Wang et al. presents a novel approach that combines iDPC-STEM experimental and first-principles techniques to investigate the rotation properties of various functional groups in the linkers of UiO-66-X. The study also examines the impact of these functional groups on the local rigidity of the framework with respect to CO2 capture.
One notable finding is the presence of functional benzene rings in the UiO-66 channels with distinct rotation properties, suggesting that the structural flexibility of the framework can be modulated by controlling the orientation of these functional groups. Furthermore, the manuscript highlights the impressive relationship between flexibility and local rigidity with CO2 capture, which has important implications for optimizing the efficiency of CO2 adsorption in metal organic frameworks.
However, there are some questions should be addressed prior to further evaluation 1) To promote consistency and clarity throughout the manuscript, it would be beneficial to include color descriptions for each icon in the atomic models presented in the figures. Specifically, it is recommended to follow the example set in Figure 4, where the color-coded icons are described in the legend.

Authors Reply:
We thank the reviewer for the constructive suggestions. We added the descriptions in figure legends. For clarification, we added the details of simulation as Fig. S9 in SI. Figures 2 and 3  3) In Figure 3 and Figure S7,  and 17.3%, respectively. As expected, the poorer image quality of UiO-66-H did result in a larger deviation. According to the reviewer's suggestion, we applied image filters to increase the quality of UiO-66-H (Fig. 3a), and the revised figure is shown below. The results of average FWHM and corresponding discussion remain the same.  4) In addition to discussing the full width at half maximum (FWHM) of the intensity profile, it would also be beneficial to examine the peaks of the line profile in more detail.

Authors Reply:
We have analyzed the intensity profile in our previous works and identified the position of carbon atoms in BDC-X linkers (Nano Lett. 2023, 23, 1787−1793. Other works have also used iDPC-STEM to reveal the local distortion of UiO-66 (Nano Lett. 2022, 24, 9928-9934).
In this work, we focused on the rotation properties of benzene ring in BDC-X linkers. Therefore, we mainly studied the FWHM of the intensity profile. In the revised manuscript, we added some discussion on the peak position and the peak shape in the line profiles.
"For UiO-66-Br, however, the signals of BDC-Br are blurred from a narrow line to a larger bright spot (Fig. 2f). The asymmetric peak shape indicates that the functional groups of -Br may be biased in one direction. Moreover, the FWHM along the long axis increased to 4.02 Å. The broadening effect is attributed to the π-flipping of benzene rings in the BDC-Br linkers." (Page 7)

Reviewer #2
This manuscript tries to show the aspect of dynamic influence, especially in the direct imaging of dynamic changes after functionalization of MOFs, in order to see correlation between local rigidity and the functional groups on the organic linkers. The (iDPC-STEM) images are beautiful and wellcombined with the measurement of FWHM in a rigorous manner and supported by a DFT study.
However, this study is focused on pristine materials without the interactions of the MOFs with CO2 provide the best values for CO2 uptake. In this sense, the proposed relationship of rotation energy and CO2 uptake does not fix suitable (see Figure 5c), this is not well supported with these data.
Authors need to carry out an in-situ study of CO2 sorption that reinforces this hypothesis. For instances, inelastic-and quasi-elastic neutron scattering is one of the most accurate techniques to study it (Chem. Sci., 2017, 8, 3109-3120). This paper is not suitable for Nature Communications.
Authors Reply: We thank the reviewers for their recognition of our images and studies, as well as for their valuable suggestions. Our work focused more on the use of iDPC-STEM to image the dynamic properties of UiO-66 with different functional groups. At the end of our work, we found a relationship between local rigidity and CO2 uptake. It can partially explain the different CO2 capture capability of UiO-66-X, but the detailed mechanism requires further investigation.
The reviewer mentioned that CO2 could possibly interacted with more polarizable atoms, such as O and N. Actually, Schwerdtfeger et al. (Mol. Phys. 2019, 117, 1200-1225 reported the polarizabilities of all elements. Using these data, we plotted the CO2 uptake against the atomic polarizabilities, as shown in Figure S12. Finally, the recommendations are inspiring and we added the two references in the revised manuscript. We agree that more investigation is required to further reveal the mechanism between rigidity and CO2 capture of UiO-66-X. In situ inelastic-and quasi-elastic neutron scattering is one of the most accurate techniques for a better understanding of the mechanism, which could provide detailed information of the lattice dynamics and molecular vibrations.
To address the issues raised by the reviewer, we made the following revisions to the text and added Fig. S12 in SI.

Reviewer #3
This manuscript used iDPC-STEM to characterize the dynamic properties of MOFs, which is novel and interesting. The authors analyzed the π-flipping properties of UiO-66 with different functional groups and systematically studied the influences on the MOF flexibility. The local rigidity of MOFs are also correlated with the CO2 capacity. This work is appealing and inspiring. Therefore, I suggest that this manuscript can be published in Nature Communications with a minor revision. The following are detailed suggestions.
1. The authors used TEM simulations to correlate with the experimental images. The simulation details were described in the main text, but it is not intuitive. Some supporting figures should be added to better illustrate the simulated models.
Authors Reply: We thank the review for valuable suggestions. We added the detailed description of the simulation in SI, and provided a model figure for the simulated regions.  2. The authors fitted the FWHM against the calculated rotation energy in Fig. 5. Although the values of fitted parameters were reported, the error range is not included. I recommend the authors to add this into SI.
Authors Reply: We added the error range of fitted parameters in SI. 3. The authors mentioned that NMR can be used to characterize the benzene rotation of BDC linkers.
And in this work, the authors proposed that iDPC-STEM can also characterize the flexibility of can provide more local information, which can hardly be obtained using NMR.
4. The authors calculated the intramolecular hydrogen bonds in BDC-CH3, BDC-NH2 and BDC-OH. The model structure of UiO-66-OH is shown in Fig. 4, while the other two structures are not included. Are there any structure differences?
Authors Reply: After structural optimization, we found that the structure of UiO-66-NH2 and UiO-66-CH3 remained unchanged (Fig. S10). The BDC-X linkers are basically the same, while the intramolecular hydrogen bonds had significantly different length. The different strength of hydrogen bonds affected the rotation properties, which was discussed in the 'theoretical explanations' section in Page 9. For clarification, we added a supplementary figure (Fig. S10) to better illustrate the structure of BDC-CH3 and BDC-NH2.
"This is attributed to the intramolecular hydrogen bond of BDC-NH2 and BDC-OH (Fig. S10)